Unifying view of stem-loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses.

Putatively, stem-loop RNA hairpins explain networks of selfish elements and RNA world remnants. Their genomic density increases with intracellular lifestyle, especially when comparing giant viruses and their virophages. RNA protogenomes presumably templated for mRNAs and self-replicating stem-loops, ancestors of modern genes and parasitic sequences, including tRNAs and rRNAs. Primary and secondary structure analyses suggest common ancestry for t/rRNAs and parasitic RNAs, parsimoniously link diverse RNA metabolites (replication origins, tRNAs, ribozymes, riboswitches, miRNAs and rRNAs) to parasitic RNAs (ribosomal viroids, Rickettsia repeated palindromic elements (RPE), stem-loop hairpins in giant viruses, their virophages, and transposable retrovirus-derived elements). Results indicate ongoing genesis of small RNA metabolites, and common ancestry or similar genesis for rRNA and retroviral sequences. Assuming functional integration of modular duplicated RNA hairpins evolutionarily unifies diverse molecules, postulating stem-loop hairpin RNAs as origins of genetic innovation, ancestors of rRNAs, retro- and Mimivirus sequences, and cells.